Installing with Docker (recommended)¶
Pulling the Docker Image¶
With Docker installed, run the following command to pull the newest version of the ImmuneDB Docker image:
$ docker pull ghcr.io/arosenfeld/immunedb
Running the Container¶
To start a shell session within the container run:
$ docker run -v $HOME/immunedb_share:/share \
-p 8080:8080 -it arosenfeld/immunedb
This will start a shell with ImmuneDB and accessory scripts pre-installed as
well as create a shared directory between the host and Docker container. Files
placed in the host’s
$HOME/immunedb_share directory and it will appear in
/share within the Docker container (and vice versa). Note
macOS is generally
/Users/your_username/ and on Linux it is generally
Additionally, MySQL stores its data in
/share/mysql_data so databases will
persist across multiple container invocations.
The location of important files are:
/root/germlines: IMGT aligned germlines for IGH, TCRA, and TCRB.
/apps/bowtie2/bowtie2: The local-alignment tool Bowtie2. This file is in the container’s
/share/configs: The recommended directory to store ImmuneDB configurations generated by
/share/mysql_data: The location MySQL (specifically MariaDB) will store its data.
/example: A set of example input data to familiarize yourself with ImmuneDB.
Once the Docker container is running, you should continue by testing out the example pipeline.